Mutation index

Figure 5.7. Amino acid index databases for physicochemical properties. The physicochemical properties, conformational parameters, and mutational indexes can be retrieved from AAindex database using keyword search.

The NPV optimization results using a GA run with different crossover and mutation indexes are presented in Table 28.2, where the number of runs performed is shown in the first column. The second column indicates the best value found in the function which was optimized, for this study the maximum NPV. The next four columns correspond to the setting that produced the best values in each run. Finally, the last two columns show the crossover and mutation indexes used in each run. 

A protein with the innocuous name p53 is one of the most frequently cited biological molecules in the Science Citation Index. The "p" in p53 stands for protein and "53" indicates a molecular mass of 53 kDa. The p53 protein plays a fundamental role in human cell growth and mutations in this protein are frequently associated with the formation of tumors. It is estimated that of the 6.5 million people diagnosed with one or another form of cancer each year about half have p53 mutations in their tumor cells and that the vast majority of these mutations are single point mutations. 

Jenkins et alf" examined the formation of mutations in the p53 gene in oesophageal cell lines following treatment with deoxycholic acid for 24 h. The authors demonstrated an increased frequency of GC to AT mutations in KYSE-30 cells at neutral pH. The lARC TP53 Mutation Database compiles (http //www-p53.iarc.fr/index.html) p53 gene mutations identified in human... 

Contraction index. We have observed that %FS declines with age in wildtype flies (12, 23) as it does in some human cardiac diseases and with gene mutations, suggesting that this index could be a reliable marker of heart performance similar to its use in mammals. Representative values for wildtype hearts are shown in Table 1 and the details are described in (23). 

Brooks, T.M., Gonzalez. L.P.. Calvert. R. Parry, J.M. (1985) The induction of mitotic gene conversion in the yeast Saccharomyces cerevisiae strain JDl. Prog. Mutat. Res.. 5, 225-228 Budavari, S., ed. (1996) The Merck Index. 12th Ed., Whitehouse Station, NJ, Merck Co, p. 287 Carere, A., Conti, G, Conti. L. Crebelli, R. (1985) Assays in Aspergillus nidulans for the... 

An issue that has already been mentioned in section 11.2 is residue numbering. Residues listed in the ATOM records of a PDB file are not necessarily numbered consecutively, may not start with residue number 1, may have an additional insertion code, and may even be negative (see [2] for details). ProSa, in contrast, uses a sequential index to address residues the first residue gets number 1, the second residue number 2, and so on. In addition, some of the residues present in a PDB file may be skipped by ProSa, for example, because they are not a standard amino acid. As a consequence, you have to make sure that the residue(s) you substitute with mutate sequence or randomise sequence really correspond to those you have in focus. One hint is the correct wild-type amino acid, as displayed in the object name of the mutant. To get a list of PDB residue numbers of a certain object and how they are mapped to the sequential index, use print residue mapping object. ... 

Gill et al. (1990) have engineered additional residues into linker L12. The result of these studies was that relatively normal filament formation was able to proceed. This indicates (but does not prove) that additional residues, which allow flexibility to be maintained, can be tolerated without compromising filament formation. However, mutations in which flexibility is lost or decreased appear to lead directly to malformation of IFs. The flexibility index for L12 is less than for linker LI, but it is clearly still an important feature of the structure. 

HIV HIV Databases Los Alamos National Laboratory Contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials (http //www.hiv.lanl.gov/content/index)... 

Listings for Chemical and Radiation Mutagenesis in Mutation Research Subject Index, 1968 and 1972... 

Iterative deconvolution Recursive deconvolution Subtractive deconvolution Positional scanning/indexing Mutational surf other methods... 

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